# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:49:31 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-[(dimethylamino)methyl]-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1cccc(c1)C(=O)Nc2cccc(c2)c3[nH]nnn3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 DN3  DN3  3-[(dimethylamino)methyl]-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide  ligand  42  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DN3
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 DN3  O14  O  O     0  -0.456   0.0363  -0.7414  -0.2618
 DN3  C13  C  C     0   0.534   0.4166   0.3991  -0.0656
 DN3  C15  C  CR6   0  -0.028   1.8643   0.7147   0.1161
 DN3  C16  C  CR16  0  -0.311   2.3113   1.7994   0.8643
 DN3  C17  C  CR16  0  -0.229   3.6739   2.0043   1.0385
 DN3  C18  C  CR16  0  -0.281   4.5892   1.1362   0.4672
 DN3  C19  C  CR6   0   0.126   4.1574   0.0483  -0.2901
 DN3  C21  C  CH2   0  -0.345   5.1635  -0.8884  -0.9037
 DN3  N22  N  NT    0  -0.399   5.9687  -1.5506   0.1046
 DN3  C23  C  CH3   0  -0.517   5.1917  -2.4839   0.8907
 DN3  C24  C  CH3   0  -0.522   7.1229  -2.1953  -0.4832
 DN3  C20  C  CR16  0  -0.326   2.7959  -0.1588  -0.4458
 DN3  N12  N  NH1   0  -0.767  -0.4184   1.4703  -0.0046
 DN3  C10  C  CR6   0   0.417  -1.8095   1.4925  -0.1195
 DN3  C11  C  CR16  0  -0.350  -2.6195   0.3711   0.0301
 DN3  C6   C  CR6   0   0.074  -4.0035   0.4972  -0.0802
 DN3  C7   C  CR16  0  -0.307  -4.5891   1.7330  -0.3346
 DN3  C8   C  CR16  0  -0.226  -3.7762   2.8466  -0.4760
 DN3  C9   C  CR16  0  -0.344  -2.4025   2.7327  -0.3728
 DN3  C2   C  CR5   0   0.509  -4.8146  -0.7031   0.0845
 DN3  N1   N  NR15  0  -0.508  -6.1467  -0.7833   0.0138
 DN3  N5   N  N     0  -0.071  -6.5183  -2.0343   0.2177
 DN3  N4   N  N     0  -0.137  -5.4487  -2.7000   0.4084
 DN3  N3   N  N     0  -0.345  -4.3762  -1.9176   0.3340
 DN3  H1   H  HCR6  0   0.263   1.6164   2.4760   1.3460
 DN3  H2   H  HCR6  0   0.264   4.0173   2.8440   1.6281
 DN3  H3   H  HCR6  0   0.256   5.6502   1.3010   0.6099
 DN3  H4   H  HCH2  0   0.214   4.6437  -1.6053  -1.5620
 DN3  H5   H  HCH2  0   0.253   5.8385  -0.3140  -1.5450
 DN3  H7   H  HCH3  0   0.234   5.8171  -2.9234   1.6688
 DN3  H8   H  HCH3  0   0.237   4.3623  -1.9756   1.3836
 DN3  H9   H  HCH3  0   0.192   4.7736  -3.3084   0.2922
 DN3  H10  H  HCH3  0   0.234   7.7334  -1.4615  -1.0112
 DN3  H11  H  HCH3  0   0.234   7.7385  -2.6397   0.3002
 DN3  H12  H  HCH3  0   0.193   6.8654  -2.9938  -1.1968
 DN3  H13  H  HCR6  0   0.257   2.4529  -1.0152  -1.0137
 DN3  H14  H  HNH1  0   0.425   0.0135   2.3815   0.0124
 DN3  H15  H  HCR6  0   0.287  -2.1955  -0.5969   0.2393
 DN3  H16  H  HCR6  0   0.257  -5.6614   1.8468  -0.4225
 DN3  H17  H  HCR6  0   0.275  -4.2172   3.8137  -0.6746
 DN3  H18  H  HCR6  0   0.283  -1.7803   3.6117  -0.4907
 DN3  H19  H  HNR5  0   0.451  -6.8410  -0.0711  -0.1627

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 DN3  C17  C18  aromatic  1.385  0.020  1.385
 DN3  C17  C16  aromatic  1.389  0.020  1.389
 DN3  C18  C19  aromatic  1.394  0.020  1.394
 DN3  C16  C15  aromatic  1.392  0.020  1.392
 DN3  C19  C21  single    1.505  0.020  1.505
 DN3  C19  C20  aromatic  1.386  0.020  1.386
 DN3  N22  C24  single    1.447  0.020  1.447
 DN3  N22  C21  single    1.450  0.020  1.450
 DN3  N22  C23  single    1.447  0.020  1.447
 DN3  C15  C20  aromatic  1.395  0.020  1.395
 DN3  C15  C13  single    1.493  0.020  1.493
 DN3  N1   N5   aromatic  1.321  0.020  1.321
 DN3  N1   C2   aromatic  1.336  0.020  1.336
 DN3  N5   N4   aromatic  1.274  0.020  1.274
 DN3  N12  C13  single    1.360  0.020  1.360
 DN3  N12  C10  single    1.396  0.020  1.396
 DN3  C11  C10  aromatic  1.391  0.020  1.391
 DN3  C11  C6   aromatic  1.394  0.020  1.394
 DN3  C13  O14  double    1.218  0.020  1.218
 DN3  C10  C9   aromatic  1.398  0.020  1.398
 DN3  C2   C6   single    1.458  0.020  1.458
 DN3  C2   N3   aromatic  1.315  0.020  1.315
 DN3  N4   N3   aromatic  1.330  0.020  1.330
 DN3  C6   C7   aromatic  1.391  0.020  1.391
 DN3  C9   C8   aromatic  1.382  0.020  1.382
 DN3  C7   C8   aromatic  1.386  0.020  1.386
 DN3  C16  H1   single    0.930  0.020  1.080
 DN3  C17  H2   single    0.930  0.020  1.080
 DN3  C18  H3   single    0.930  0.020  1.080
 DN3  C21  H4   single    0.970  0.020  1.090
 DN3  C21  H5   single    0.970  0.020  1.090
 DN3  C23  H7   single    0.970  0.020  1.090
 DN3  C23  H8   single    0.970  0.020  1.090
 DN3  C23  H9   single    0.970  0.020  1.090
 DN3  C24  H10  single    0.970  0.020  1.090
 DN3  C24  H11  single    0.970  0.020  1.090
 DN3  C24  H12  single    0.970  0.020  1.090
 DN3  C20  H13  single    0.930  0.020  1.080
 DN3  N12  H14  single    0.860  0.020  1.020
 DN3  C11  H15  single    0.930  0.020  1.080
 DN3  C7   H16  single    0.930  0.020  1.080
 DN3  C8   H17  single    0.930  0.020  1.080
 DN3  C9   H18  single    0.930  0.020  1.080
 DN3  N1   H19  single    0.860  0.020  1.020

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 DN3  N12  C13  C15  115.06  3.000
 DN3  N12  C13  O14  123.58  3.000
 DN3  C15  C13  O14  121.35  3.000
 DN3  C20  C15  C16  119.35  3.000
 DN3  C20  C15  C13  117.79  3.000
 DN3  C16  C15  C13  122.80  3.000
 DN3  H1   C16  C17  118.79  3.000
 DN3  H1   C16  C15  121.34  3.000
 DN3  C17  C16  C15  119.84  3.000
 DN3  H2   C17  C18  120.10  3.000
 DN3  H2   C17  C16  119.62  3.000
 DN3  C18  C17  C16  120.28  3.000
 DN3  H3   C18  C19  119.58  3.000
 DN3  H3   C18  C17  119.85  3.000
 DN3  C19  C18  C17  120.57  3.000
 DN3  C20  C19  C21  121.19  3.000
 DN3  C20  C19  C18  118.81  3.000
 DN3  C21  C19  C18  120.00  3.000
 DN3  H5   C21  H4   106.39  3.000
 DN3  H5   C21  N22  107.74  3.000
 DN3  H4   C21  N22  112.31  3.000
 DN3  H5   C21  C19  108.94  3.000
 DN3  H4   C21  C19  109.43  3.000
 DN3  N22  C21  C19  111.82  3.000
 DN3  C24  N22  C23  111.21  3.000
 DN3  C23  N22  C21  111.97  3.000
 DN3  C24  N22  C21  111.34  3.000
 DN3  H9   C23  H8   107.81  3.000
 DN3  H9   C23  H7   107.68  3.000
 DN3  H8   C23  H7   107.55  3.000
 DN3  H9   C23  N22  113.05  3.000
 DN3  H8   C23  N22  110.70  3.000
 DN3  H7   C23  N22  109.85  3.000
 DN3  H12  C24  H11  107.57  3.000
 DN3  H12  C24  H10  107.76  3.000
 DN3  H11  C24  H10  107.81  3.000
 DN3  H12  C24  N22  113.56  3.000
 DN3  H11  C24  N22  109.87  3.000
 DN3  H10  C24  N22  110.08  3.000
 DN3  H13  C20  C19  119.20  3.000
 DN3  H13  C20  C15  119.65  3.000
 DN3  C19  C20  C15  121.15  3.000
 DN3  H14  N12  C10  114.44  3.000
 DN3  H14  N12  C13  116.71  3.000
 DN3  C10  N12  C13  128.38  3.000
 DN3  C9   C10  C11  119.18  3.000
 DN3  C9   C10  N12  116.85  3.000
 DN3  C11  C10  N12  123.95  3.000
 DN3  H15  C11  C6   119.17  3.000
 DN3  H15  C11  C10  121.06  3.000
 DN3  C6   C11  C10  119.77  3.000
 DN3  C2   C6   C7   121.19  3.000
 DN3  C7   C6   C11  120.85  3.000
 DN3  C2   C6   C11  117.96  3.000
 DN3  H16  C7   C8   119.24  3.000
 DN3  H16  C7   C6   121.71  3.000
 DN3  C8   C7   C6   119.05  3.000
 DN3  H17  C8   C9   119.52  3.000
 DN3  H17  C8   C7   119.88  3.000
 DN3  C9   C8   C7   120.60  3.000
 DN3  H18  C9   C8   119.72  3.000
 DN3  H18  C9   C10  119.73  3.000
 DN3  C8   C9   C10  120.55  3.000
 DN3  N3   C2   N1   106.67  3.000
 DN3  N3   C2   C6   126.61  3.000
 DN3  N1   C2   C6   126.72  3.000
 DN3  H19  N1   N5   120.09  3.000
 DN3  H19  N1   C2   130.69  3.000
 DN3  N5   N1   C2   109.21  3.000
 DN3  N4   N5   N1   106.37  3.000
 DN3  N3   N4   N5   111.18  3.000
 DN3  N4   N3   C2   106.57  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 DN3  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 DN3  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 DN3  CONST_03  C19  C18  C17  C16     0.00   0.0  0
 DN3  CONST_04  C19  C20  C15  C16     0.00   0.0  0
 DN3  CONST_05  C20  C19  C18  C17     0.00   0.0  0
 DN3  CONST_06  C20  C15  C16  C17     0.00   0.0  0
 DN3  CONST_07  C2   C6   C11  C10   180.00   0.0  0
 DN3  CONST_08  C7   C6   C11  C10     0.00   0.0  0
 DN3  CONST_09  C7   C8   C9   C10     0.00   0.0  0
 DN3  CONST_10  C8   C9   C10  C11     0.00   0.0  0
 DN3  CONST_11  N1   C2   C6   C11   180.00   0.0  0
 DN3  CONST_12  N3   C2   C6   C11     0.00   0.0  0
 DN3  CONST_13  C8   C7   C6   C11     0.00   0.0  0
 DN3  CONST_14  C9   C10  C11  C6      0.00   0.0  0
 DN3  CONST_15  N5   N1   C2   C6    180.00   0.0  0
 DN3  CONST_16  N4   N3   C2   C6    180.00   0.0  0
 DN3  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 DN3  CONST_18  N1   C2   C6   C7      0.00   0.0  0
 DN3  CONST_19  N3   C2   C6   C7    180.00   0.0  0
 DN3  CONST_20  C2   C6   C7   C8    180.00   0.0  0
 DN3  CONST_21  N4   N5   N1   C2      0.00   0.0  0
 DN3  CONST_22  N5   N4   N3   C2      0.00   0.0  0
 DN3  CONST_23  N3   N4   N5   N1      0.00   0.0  0
 DN3  CONST_24  N4   N3   C2   N1      0.00   0.0  0
 DN3  CONST_25  N3   C2   N1   N5      0.00   0.0  0
 DN3  CONST_26  C17  C16  C15  C13   180.00   0.0  0
 DN3  CONST_27  C19  C20  C15  C13   180.00   0.0  0
 DN3  CONST_28  C21  C19  C20  C15   180.00   0.0  0
 DN3  CONST_29  C21  C19  C18  C17   180.00   0.0  0
 DN3  CONST_30  C6   C11  C10  N12   180.00   0.0  0
 DN3  CONST_31  C8   C9   C10  N12   180.00   0.0  0
 DN3  CONST_32  H2   C17  C16  C15   180.00   0.0  0
 DN3  CONST_33  H3   C18  C17  C16   180.00   0.0  0
 DN3  CONST_34  H13  C20  C15  C16   180.00   0.0  0
 DN3  CONST_35  H1   C16  C17  C18   180.00   0.0  0
 DN3  CONST_36  H17  C8   C9   C10   180.00   0.0  0
 DN3  CONST_37  H18  C9   C10  C11   180.00   0.0  0
 DN3  CONST_38  H16  C7   C6   C11   180.00   0.0  0
 DN3  CONST_39  H19  N1   C2   C6      0.00   0.0  0
 DN3  CONST_40  H15  C11  C6   C7    180.00   0.0  0
 DN3  CONST_41  C10  N12  C13  C15   180.00   0.0  0
 DN3  CONST_44  H14  N12  C10  C11   180.00   0.0  0
 DN3  CONST_45  C10  N12  C13  O14     0.00   0.0  0
 DN3  Var_01    C16  C15  C13  O14  -152.18  30.0  2
 DN3  Var_02    N22  C21  C19  C18    61.86  30.0  2
 DN3  Var_03    C24  N22  C21  C19  -166.49  30.0  2
 DN3  Var_04    H10  C24  N22  C21    58.44  30.0  3
 DN3  Var_05    H7   C23  N22  C21  -177.15  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 DN3  plan-1  C6   0.020
 DN3  plan-1  C2   0.020
 DN3  plan-1  N1   0.020
 DN3  plan-1  N5   0.020
 DN3  plan-1  N4   0.020
 DN3  plan-1  N3   0.020
 DN3  plan-1  H19  0.020
 DN3  plan-2  C13  0.020
 DN3  plan-2  C15  0.020
 DN3  plan-2  C16  0.020
 DN3  plan-2  C17  0.020
 DN3  plan-2  C18  0.020
 DN3  plan-2  C19  0.020
 DN3  plan-2  C21  0.020
 DN3  plan-2  C20  0.020
 DN3  plan-2  H1   0.020
 DN3  plan-2  H2   0.020
 DN3  plan-2  H3   0.020
 DN3  plan-2  H13  0.020
 DN3  plan-3  N12  0.020
 DN3  plan-3  C10  0.020
 DN3  plan-3  C11  0.020
 DN3  plan-3  C6   0.020
 DN3  plan-3  C7   0.020
 DN3  plan-3  C8   0.020
 DN3  plan-3  C9   0.020
 DN3  plan-3  C2   0.020
 DN3  plan-3  H15  0.020
 DN3  plan-3  H16  0.020
 DN3  plan-3  H17  0.020
 DN3  plan-3  H18  0.020
 DN3  plan-4  O14  0.020
 DN3  plan-4  C13  0.020
 DN3  plan-4  C15  0.020
 DN3  plan-4  N12  0.020
 DN3  plan-4  C10  0.020
 DN3  plan-4  H14  0.020

